37 commits
| Author | SHA1 | Message | Date | |
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Trevon
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b6e6cd38f8 |
fix(topology): make louvain moves independent of hash order (#313)
makeAdjacency filled each neighbor list in PairWeightMap (unordered_map) order, and the local-move loop took the first best community from an unordered_map. Both orders differ between libc++ and libstdc++, so the same corpus produced different communities on macOS and Linux, and topology_representative_rule failed on macOS. Neighbor lists are now sorted by index and equal-gain moves go to the smaller community id. The louvain characterization is regenerated; macOS and Linux now give the same result. Signed-off-by: trvon <me@trevon.dev> |
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Trevon
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beef87e66c |
bench(retrieval): seed one-way kNN semantic edges on request (#308)
Some checks failed
Fuzz Smoke / libFuzzer smoke (push) Has been cancelled
Benchmark seeding wrote only mutual neighbor pairs. The connected topology engine keeps every reciprocal edge at or above min_edge_score inside its component, so with mutual-only seeding no raw neighbor crosses a cluster boundary and the engine builds no roads. The Eval 2 smoke showed roads_absent on every connected-engine query. The daemon stores one-way kNN edges (GraphComponent treats them as ordinary non-mutual neighbors). YAMS_BENCH_SEED_SEMANTIC_DIRECTED=1 seeds them too, as single directed edges. Default off keeps existing plans unchanged. The pair loop moves into buildSemanticNeighborSeedEdges in the bench support library, sorted by (source, target), with a unit test for both modes. A topology test pins the mutual-only case: no roads on the connected engine until a one-way edge exists. Signed-off-by: trvon <me@trevon.dev> |
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Trevon
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cfb70f7bb9 |
feat(topology): ordered members (#306)
Give every cluster with at least two members a walk order: `ClusterArtifact::orderedMembers`, a uint32 permutation over the hash-sorted `memberDocumentHashes`, plus `orderKind`. Three kinds, each deterministic with ties resolved to the smaller member hash: - Time: ascending `TopologyDocumentInput::eventTime`; members without a time last, by hash. - Session: grouped by `sessionId`; groups ordered by earliest event time (groups with no time after those with one), then session id; inside a group by time then hash; unsessioned members last, by time then hash. - SimilarityChain: greedy nearest-neighbor tour by cosine over the members' embeddings, starting from the cluster representative (`medoid`, else the smallest-hash usable member); members without a usable embedding last, by hash. The knob is `TopologyBuildConfig::roadOrder`, resolved from TOML `topology.road_order` = none|time|session|similarity_chain through the topology.* resolver block and `TopologyManager::setRoadOrder`, threaded into the build config like `roadMaxPerCluster`. Orders are computed after boundary spill so they cover replicas, at full build in every engine and for the rebuilt clusters of a connected-engine incremental update; untouched clusters keep theirs (a kind change reaches them on the next full rebuild, like the representative rule) and `none` clears every order. Orders are independent of `roadMaxPerCluster`. Orders persist in the road sidecar, now version 3: after the roads, u32 count, then per ordered cluster u32 cluster-id table index, u32 kind, u32 length and the permutation as u32 indices. A sidecar without orders is still written as v2, so roads-only sidecars are byte-identical to the previous layout; v1 and v2 decode with no orders, and the envelope gains `member_order_count`. The sidecar is written when the batch has roads or at least one ordered cluster. On load each order is validated on its own (`attachTopologyMemberOrders`: cluster exists, kind not none, permutation covers the members exactly once); an invalid entry drops only that cluster's order and appends `<token>:<clusterId>` to the new load-time diagnostic `TopologyArtifactBatch::orderUnavailableReason`. Roads never lose anything to an order error and vice versa. The main snapshot codec, the routing construction, representation and road fingerprints never see orders, so the default `none` leaves the snapshot payload, the sidecar and every fingerprint byte-identical. No search consumer yet; the road walk lands separately. Tests: tests/unit/topology/topology_ordered_members_catch2_test.cpp (permutation validator tokens, time order with missing times, session grouping and group tie-break, hand-computed greedy chain from the medoid on a five-point fixture with fallback start, unusable members and exact ties, every engine stores valid permutations of every kind including over spill replicas, default none byte-identical payload/sidecar/fingerprints, sidecar v3 round trip plus hand-built v2 bytes and corrupt-section rejection, per-cluster attach validation with reasons, store round trip with orders-only sidecars, invalid order dropped with reason while roads and other orders stay, incremental update keeps untouched orders and recomputes rebuilt ones), plus resolver and manager setter coverage. Signed-off-by: trvon <me@trevon.dev> |
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Trevon
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111988c6e4 |
feat(topology): typed event time and session for topology inputs (#305)
* feat(topology): typed event time and session for topology inputs Add `eventTime` (epoch seconds, UTC) and `sessionId` to `TopologyDocumentInput`. The extractor fills them from two documented metadata keys: `event_time` (integer epoch seconds, or ISO-8601 `YYYY-MM-DD` / `YYYY-MM-DD[T ]HH:MM[:SS[.frac]][Z|±HH:MM]`, naive datetimes are UTC) takes precedence over the document createdTime; an unparsable value is skipped with a debug log, never an error, and a zero createdTime leaves the field unset. `session_id` is copied verbatim and empty when absent. The keys are only consulted when the extraction loads metadata; otherwise createdTime is the only source. `parseTopologyEventTime` is public for tests and future callers; the calendar math is Hinnant's days_from_civil with range-checked fields. Extraction stats count the event time source and invalid values. Nothing downstream reads the fields yet. Artifacts, codecs and both routing fingerprints are unchanged, which the new test pins. Tests (tests/unit/topology/topology_input_event_time_catch2_test.cpp): parser accept/reject tables, metadata precedence over createdTime, invalid ignored, session_id, includeMetadata=false fallback, and byte-identical snapshot payload plus equal construction and road fingerprints with and without the typed fields. Signed-off-by: trvon <me@trevon.dev> * bench(longmemeval): event_time and session_id metadata, round docs, haystack sidecar Every exported corpus document now carries `metadata.event_time` (ISO-8601, normalized from the LongMemEval `YYYY/MM/DD (Day) HH:MM` haystack date, first-seen date per session) and `metadata.session_id`. Document ids, titles, texts, queries and qrels are unchanged in the default mode. `--round-docs` adds one document per session round (`<sid>__r<n>`): a user turn opens a round and the replies that follow join it; a leading assistant turn is its own round. Round docs share the session's `event_time`/`session_id` and add `round_index`; qrels stay at the session level. `--full-haystack` also writes `haystacks.jsonl`, one line per question with `haystack_session_ids` and the normalized `haystack_dates`, so per-question membership survives the global corpus deduplication (the 2026-10-10 preflight lost it). The converter is split into `convert` / `write_outputs`; `--self-test` runs both on a three-session synthetic fixture without a download and is the regression check for the default output. Signed-off-by: trvon <me@trevon.dev> * bench(retrieval): carry BEIR corpus metadata onto ingested documents `retrieval_quality_bench` ingests the BEIR corpus as a directory, which cannot carry per-file metadata, so `event_time`, `session_id` and `round_index` from corpus.jsonl never reached the topology extractor. `BEIRDocument::metadata` now holds the corpus line's `metadata` object (strings as is, numbers and booleans stringified; both the generic and the SciFact loader read it), and `applyBenchmarkDocumentMetadata` copies it onto the stored documents matched by exact file path through the metadata repository (`ON CONFLICT DO UPDATE`, so warm caches can repeat it). The bench runs it after the ingest wait, for cold and reused corpora alike, and logs how many documents were updated or not found. Tests: loader parses and coerces metadata; apply helper writes the keys, skips documents without metadata, counts missing ones and is idempotent against a real MetadataRepository. The portability allowlist entries for the two touched bench files are re-pointed at their shifted lines; no raw environment read was added. Signed-off-by: trvon <me@trevon.dev> --------- Signed-off-by: trvon <me@trevon.dev> |
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Trevon
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f7f1a09865 |
feat(topology): incremental roads (#303)
Maintain cluster roads across incremental rebuilds instead of clearing them. `ConnectedComponentTopologyEngine::updateArtifacts` now keeps the roads between clusters the update did not touch, drops every road with an endpoint in a removed or rebuilt cluster (reused ids included), and recomputes the rebuilt clusters' roads from the dirty region's raw neighbor lists against the merged memberships, so a region document's neighbor in an untouched cluster yields that road in both orientations. Each source then re-ranks its top-K over the union with PR 6's order and tie-break (weight desc, target id asc). Only the region's neighbor lists are available during an update, so a cross-boundary edge is observed from one side; the out-of-region target is credited with the mirror observation its own list would have added. That is exact on a symmetric neighbor graph and the stated approximation otherwise. An untouched source can only re-rank the roads its last full build kept, so the result is derived, not full. Provenance on the batch: `roadsIncrementalPasses` counts passes since the last full accumulation (0 = full roads) and `roadsFullBuildEpoch` is the `topologyEpoch` of the snapshot that accumulation produced. A full build leaves both at 0; an update sets the epoch from `existing` when its roads were full and carries it forward otherwise. The fields ride in the road sidecar header, now version 2 (u64 epoch, u32 passes after the snapshot id); version 1 sidecars decode with both at 0, the envelope format string is unchanged, and the main v1 payload and the routing construction fingerprint do not see them. The store copies them both ways. Roads off (`road_max_per_cluster = 0`, the default) still yields no roads and zero provenance, so default behavior is unchanged. `topology_build_utils.h` splits `accumulateClusterRoads` into pair-weight accumulation (with the optional observed-document set that drives mirroring), orientation and ranking, and adds `deriveIncrementalRoads` over those pieces; the full-build path passes no observed set and is unchanged. Louvain and k-means `updateArtifacts` rebuild the supplied input from scratch, so their roads are full roads for that batch with zero passes; the test states and checks that property for them. Tests: tests/unit/topology/topology_roads_incremental_catch2_test.cpp (roads off through an update, full-build provenance, kept/retired/ recomputed roads with mirrored weights on a four-cluster graph, top-K re-ranking over kept and recomputed roads, derivation without prior roads, a property test over seeded planted-cluster symmetric graphs with cross-edge rewiring and member moves comparing incremental roads to a from-scratch build after each of several dirty regions, a tight-top-K property for rebuilt sources and derived weights, and the alternate engines), plus sidecar v2 round trip, hand-built v1 decode, future version rejection and store round trip of the provenance in topology_road_sidecar_catch2_test.cpp. Signed-off-by: trvon <me@trevon.dev> |
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Trevon
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e84ced261b |
feat(topology): road sidecar persistence (#302)
Persist `TopologyArtifactBatch::roads` in a sidecar knowledge-graph node,
`topology:roads:<snapshotId>` of type `topology_road_snapshot`, instead
of growing the main snapshot codec. The sidecar has its own binary magic
('Y','A','M','R'), version 1, and a Zstd JSON envelope with
`format = "topology_roads_zstd_v1"`. The main snapshot stays a plain v1
payload, byte-identical with roads on or off, so memory-sync replicas on
older peers keep decoding it, and an unknown node type is simply never
read by an old store. `deserializeTopologyBatchCompressed` now rejects an
envelope whose `format` it does not know instead of treating it as legacy
raw JSON.
Header layout (little-endian): u32 magic, u32 version, u32 maxPerCluster,
u32 reserved, string snapshotId, u32 cluster-id table count + strings,
u32 road count, then per road u32 from index, u32 to index, f64 weight.
`TopologyArtifactBatch::roadMaxPerCluster` records the bound the builder
applied so the header can carry it; both engines set it.
The store writes the sidecar right after the snapshot node and before
the `topology:snapshot:latest` pointer, so the pointer remains the commit
point: an injected sidecar failure leaves the previous snapshot current.
Retention deletes each pruned snapshot's sidecar with it, and re-storing
a snapshot id without roads removes its stale sidecar. Loading is
optional and soft: a missing sidecar yields empty roads with no error; an
undecodable or invalid one (snapshot mismatch, endpoint not a cluster,
self loop, negative or non-finite weight, more roads per source than the
declared top-K) drops the roads and records
`TopologyArtifactBatch::roadUnavailableReason`, surfaced on the routing
session and as the `topology_road_unavailable_reason` debug key, while
the snapshot still loads and routes.
`topologyRoadFingerprint(batch)` gives roads their own order-independent
identity for cache provenance; the routing construction fingerprint is
unchanged and stays road-free through the persisted path.
Lean (formal/topology/Yams/Topology/Artifacts.lean): `ClusterRoad`,
`WellFormedRoads` (endpoints in clusters, no self loop, non-negative
weight, bounded per source), `constructionIdentity`, and lemmas that the
construction identity and `WellFormedBatch` are independent of roads and
that an empty road layer is well formed. Checked with lake (lean 4.31.0).
Tests: tests/unit/topology/topology_road_sidecar_catch2_test.cpp (codec
round trip, foreign/truncated payload rejection, main payload identical
on/off, validation reasons, store round trip, missing sidecar, every
corrupt-sidecar case with routing still admitted, write-before-pointer,
retention, fingerprints through the persisted path) and the extended
fingerprint invariance test in topology_roads_catch2_test.cpp.
`road_to` knowledge-graph edges are deferred until a consumer needs them.
Signed-off-by: trvon <me@trevon.dev>
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Trevon
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dcdeaa81d0 |
feat(topology): accumulate roads at build (in memory) (#301)
Add cluster roads: undirected cluster-to-cluster links whose weight is
the sum of every raw neighbor observation between members of two
clusters. The shared helper `accumulateClusterRoads` in
topology_build_utils.h reads `TopologyDocumentInput::neighbors` before
the reciprocal/minEdgeScore filter, because the connected engine's
filtered adjacency only carries cross-cluster edges where an oversized
component was split, and k-means never consults the graph.
Each cluster keeps its top-K roads (weight desc, then target cluster id
asc) as `ClusterRoad {fromClusterId, toClusterId, weight}` on
`TopologyArtifactBatch::roads`, sorted by source cluster. Both the
connected engine and buildBatchFromAssignment (kmeans/louvain) call it;
an incremental update clears roads until the next full rebuild.
The knob is `TopologyBuildConfig::roadMaxPerCluster`, resolved from
TOML `topology.road_max_per_cluster` through the topology.* resolver
block and `TopologyManager::setRoadMaxPerCluster`. The default 0
computes no roads; the binary codec and the routing construction
fingerprint ignore the field, so existing snapshots and fingerprints
are unchanged with roads on or off.
Tests: tests/unit/topology/topology_roads_catch2_test.cpp (raw vs
filtered neighbors, top-K and tie-break, order independence, both
orientations, out-of-batch and non-finite scores, kmeans and louvain,
codec bytes and fingerprint unchanged), plus resolver and manager
setter coverage.
Signed-off-by: trvon <me@trevon.dev>
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Trevon
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c26294a938 |
feat(topology): opt-in medoid representative and BQ rotation (#277)
* test(topology): characterize degree representatives and raw BQ sign bits
Pin the current behaviour before adding opt-in representative and BQ
rotation options:
- connected, louvain and kmeans engines on a skewed cluster (dense
clique plus a weak-edge hub): medoid hash, score, extra routing
representatives and roles;
- equal-degree ties go to the smaller document hash;
- the unrotated BinaryQuantizedIndex matches a raw-coordinate sign-bit
reference, with and without a prefix dimension.
Signed-off-by: trvon <me@trevon.dev>
* feat(topology): add an opt-in medoid representative rule
topology.representative_rule = degree (default) | medoid selects how a
cluster's representative document is chosen. Degree keeps the max
within-cluster weighted degree. Medoid picks the member minimising
sum_j sqrt(max(0, 2(1 - cos))) over the other members.
- one shared helper, applyRepresentativeRule(), is called by the
connected, louvain and kmeans engines after their unchanged degree
choice; medoid falls back to it without usable geometry;
- clusters above 256 usable members are searched on a deterministic
hash-ordered stride sample (kMedoidRepresentativeMaxMembers);
- ties within 1e-9 go to the smaller document hash;
- with medoid, farthest-first extra routing representatives are seeded
from the medoid instead of the centroid;
- the rule is stored in the formerly reserved first header byte of the
binary snapshot (0 = degree, so old snapshots keep their meaning) and
extends the construction fingerprint only when it is not degree;
- search debug stats report topology_representative_rule.
Signed-off-by: trvon <me@trevon.dev>
* feat(topology): add an opt-in randomized Hadamard rotation for BQ routing
search.topology.bq_rotation = none (default) | fwht selects the rotation
applied before the centroid BQ shortlist takes sign bits. Raw-coordinate
sign bits make cos(pi * h / d) a poor estimate on anisotropic embeddings;
after x -> (1/sqrt(n)) H D [x; 0] every bit is a random hyperplane.
- RandomizedHadamardRotation in yams/vector: fixed splitmix64 sign
diagonal plus an in-place FWHT, zero-padded to a power of two; Simeon's
FWHT projection works on int32 sketches with row subsampling, so a
small local transform is used instead;
- BinaryQuantizedIndex::build() takes the rotation and seed, rotates
stored vectors before the prefix is taken, and rotates every float
query itself, so centroids and queries always share one seed
(kDefaultBinaryRotationSeed);
- the routing snapshot cache records bqRotation and bqRotationSeed and
rebuilds the route index when either differs;
- the routing policy fingerprint changes only for a non-default rotation;
- search debug stats report topology_route_bq_rotation.
Signed-off-by: trvon <me@trevon.dev>
* test(bench): map representative rule and BQ rotation arm knobs
Harness-only env knobs written into the isolated benchmark config.toml,
so arms go through ConfigResolver like the other topology settings:
- YAMS_BENCH_TOPOLOGY_REPRESENTATIVE_RULE=degree|medoid
-> [topology] representative_rule
- YAMS_BENCH_TOPOLOGY_BQ_ROTATION=none|fwht
-> [search.topology] bq_rotation, next to bq_candidate_limit and
bq_prefix_dim
The debug-file setup entry records the requested values; per-query
search_stats carry the effective topology_representative_rule and
topology_route_bq_rotation. Portability allowlist lines are shifted for
the inserted code.
Signed-off-by: trvon <me@trevon.dev>
---------
Signed-off-by: trvon <me@trevon.dev>
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Trevon
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4ec044afd6 |
fix(vector): rank vec0 by cosine on unit-normalized copies (#275)
* test(vector): pin vec0 ranking to cosine order on non-unit rows vec0 ranks by L2 distance, which matches cosine order only for unit vectors. Insert rows whose L2 order disagrees with cosine order and assert vec0 returns cosine order, agrees with the exact cosine scan, skips zero rows and rejects a zero query. Pins a vector-enabled env so the cases run under the CI test env. Signed-off-by: trvon <me@trevon.dev> * fix(vector): rank vec0 by cosine on unit-normalized copies vec0 ranks by L2 distance, which matches cosine order only when both sides are unit length. Stored rows reach the vectors table at whatever magnitude the provider, config, import or sync produced, and the vec0 aux table copied them as-is, so vec0 selected and ordered rows differently from the Simeon PQ and exact cosine paths. The vec0 table is a derived index rebuilt from vectors.embedding, so write the unit direction into it and leave the source blob, which export/sync and exact scoring read, untouched. Normalize the query the same way. Zero rows are left out of vec0 and never match; a zero or non-finite query is rejected as the exact scan rejects it. Returned rows are ordered by their cosine score with the PQ tie-break. No schema change. The aux table is rebuilt on first use in each process (ready dims are in-memory), so existing non-unit rows are normalized on the next rebuild without a repair step. Signed-off-by: trvon <me@trevon.dev> * test(topology): pin the k-means stored centroid to the unit direction Spherical k-means assigns against unit centroids but stored the shorter arithmetic mean. Assert the stored centroid is unit length along the member mean direction, with and without boundary spill. Add a SOAR case showing that with unit centroids the spill follows angular distance, and that a short mean centroid reorders the candidates. Reformat the touched k-means test file to the lint formatter. Signed-off-by: trvon <me@trevon.dev> * fix(topology): store the unit k-means centroid The k-means engine clusters by cosine against normalized centroids, then stored the unnormalized member mean as centroidEmbedding. Routing reads the centroid by cosine and does not care, but SOAR boundary spill measures Euclidean residuals against it. A loose cluster's short mean adds a radial term to those residuals, so spill candidates were ranked in a different space from the one the clusters were built and routed in. Store the unit mean direction for k-means, which is the converged Lloyd centroid. Connected-component and Louvain keep the arithmetic mean, as their tests and contract require. Correct the stale field comment. Signed-off-by: trvon <me@trevon.dev> --------- Signed-off-by: trvon <me@trevon.dev> |
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trvon
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39af8dfc35
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feat(topology): select the dirty-region expansion mode from config
TopologyBuildConfig::dirtyRegionExpansion had no path from config: TopologyManager never set it, so every incremental rebuild used the default (PriorClusterAndNeighbors) and the NeighborsOnly and Adaptive branches in ConnectedComponentTopologyEngine::defineDirtyRegion never ran. It now follows the typed-config path the other topology knobs use: [topology] dirty_region_expansion = "neighbors_only" # or prior_cluster_and_neighbors, adaptive ConfigResolver::resolveTopologyEnginePolicy parses it (case-insensitive; an unknown value is logged and ignored, never guessed), ServiceManager::configureTopologyRuntime applies it, and TopologyManager passes it to the incremental dirty-region config and the build config. dirtyRegionExpansionModeName / parseDirtyRegionExpansionMode give the enum one spelling. Adaptive currently takes every branch PriorClusterAndNeighbors takes, so selecting it changes nothing yet. A characterization test pins that, so a real adaptive policy has to change it deliberately. Tests (the manager test fails with the TopologyManager line removed): - topology_manager: an incremental rebuild seeded from a clustered document reports "prior_cluster+neighbors" by default and "neighbors" under neighbors_only; - config_resolver: a recognized mode resolves; an unknown or absent one leaves the default; - topology_baseline: NeighborsOnly excludes prior-cluster members; Adaptive matches the default; names round-trip. Found by pipe's experimental C++ front end: NeighborsOnly and Adaptive were compared in topology_baseline.cpp but never produced anywhere. |
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trvon
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6e1a5262b5
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fix(topology): keep rebuilding when the latest snapshot is undecodable
storeBatch loads the previous snapshot only to find documents that left the topology, but returned early when it could not decode it, so one corrupt payload blocked every future topology write. On a decode error, log and store the new snapshot without clearing dropped documents' keys; other load errors still propagate. |
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trvon
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14057afbf8
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feat(topology): materialize clusters in the knowledge graph
Topology wrote back only an opaque compressed snapshot node, so yams graph, explore and graph expansion could not traverse clusters, and every rebuild added another full snapshot node that was never removed. Each stored snapshot now replaces the cluster graph in one KG write batch before the latest pointer flips: topology:cluster:<id> nodes with size, level, persistence, cohesion and density; document member_of edges weighted by persistence, medoid_of edges, overlaps edges for boundary-spill memberships, and subcluster_of hierarchy edges. After the pointer flips, snapshot nodes beyond the newest three are removed; the one the pointer names is always kept. |
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trvon
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1a74d4c73e
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fix(graph): make semantic_neighbor reciprocity mean mutual kNN
Every kNN edge was also written in reverse, so each semantic_neighbor edge looked reciprocal and topology's reciprocalOnly filtering, SGC smoothing over reciprocal edges, and graph reciprocity metrics filtered nothing. Write only the edge from a document to each of its k nearest neighbours; a reverse edge now exists exactly when the pair is mutual. Semantic maintenance pruned one-way edges on the assumption that edges were symmetric; with directed kNN edges that would erase every non-mutual neighbour, so it now removes only self-loops (and no longer reports a fabricated community size for the scoped pass). Edge reads truncated by insertion order: getEdgesBidirectional sorted by id and getEdgesTo had no order, so a LIMIT kept arbitrary or oldest edges. Both now return strongest first, and the topology extractor reads a document's own neighbours separately from its incoming edges so a hub's many incoming edges cannot evict them. Existing databases keep their mirrored edges until the semantic neighbour graph is rebuilt. |
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trvon
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c990b4878d
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fix(topology): make SGC smoothing deterministic and skip ragged inputs
Edges were emitted in unordered_map iteration order, so float accumulation, and the smoothed embeddings feeding snapshot fingerprints, varied with input order. Order each neighbor list by document hash. Documents whose embedding is missing or of a different dimension were treated as zero vectors yet still added degree, damping their neighbors. Exclude them from the propagation graph. Hop 0 now reads the inputs directly, dropping one n*dim buffer for single-hop smoothing. Add closed-form checks against D^-1/2 (A+I) D^-1/2 for one and two hops. |
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trvon
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da3e398b5c
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fix(topology): keep exhaustive routing when BQ cannot score a query
The BQ branch cleared every route candidate before searching, so a query the index could not quantize (shorter than the indexed dimension) left only sparse-seeded clusters. The BQ fallback runs whenever the dense ANN index is absent, which made this reachable in production. Only narrow candidates when BQ returns a shortlist, matching the dense ANN branch, and document that the SimHash similarity estimate is an ordering proxy for raw sign bits. |
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trvon
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fff24242fd
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fix(topology): make the latest pointer the storeBatch commit point
storeBatch wrote per-document keys before the snapshot node, so a failure in between left documents pointing at a snapshot that was never persisted. Write the snapshot node first and the latest pointer last so a partial store leaves the previous snapshot authoritative. Remove only the two per-document keys still written, in one transaction via a new removeMetadataBatch, and stop the membership slow path from reading structural keys that migration 41 prunes. |
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trvon
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522c33a9ca
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fix(topology): share one resident snapshot behind a lock
The metadata store cached the latest batch in an unguarded mutable optional that search threads read and wrote, and handed out a full copy on every loadLatest, so search kept the snapshot resident twice. Publish the latest batch and its membership index as one immutable shared snapshot under a mutex, add loadLatestShared to hand it out without copying, and feed the routing snapshot cache from it. Historical loads no longer displace the resident latest snapshot, and a reader that raced a write never installs the older batch. |
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trvon
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5267b32775
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fix(topology): bound snapshot decode against corrupt payloads
Validate every element count against the remaining payload before reserving, reject trailing bytes, type-check envelope fields, bound the untrusted uncompressed_bytes hint, read the magic little-endian, and convert legacy JSON type errors into Result errors instead of throwing. |
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trvon
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c3b667ee40
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feat(retrieval): SGC topology smoothing, Matryoshka BQ prefix, and fragment outer-MaxSim
Implement three research-backed retrieval optimizations connecting
paperbridge literature findings with YAMS subsystems:
1. SGC Feature Smoothing (Proposal A):
- Add sgcHops and sgcNormalize to TopologyBuildConfig.
- Diffuse document embeddings across reciprocal nearest-neighbor graph
edges prior to clustering, formalizing Lean SGC.lean.
- Re-normalize diffused embeddings to preserve unit hypersphere metric geometry.
- Wire into ConnectedComponent, Louvain, and KMeans topology engines.
2. Matryoshka Prefix Binary Quantization (Proposal C):
- Add maxDimensions parameter to BinaryQuantizer::quantize and
maxPrefixDimension to BinaryQuantizedIndex::build.
- Support fast 64-bit word-aligned prefix Hamming shortlisting in
SparseGuidedClusterRouter via bqPrefixDimension.
3. Fragment Outer-MaxSim Reranker (Proposal B):
- Implement SimeonScoringMode { SingleVectorCosine, FragmentOuterMaxSim }
in SimeonModelProvider.
- Add extractDocumentFragments and late-interaction outer-MaxSim scoring
inspired by ColBERTv2/PLAID/SPLATE to prevent relevance dilution in long docs.
- Expose simeonRerankOuterMaxSim on SearchEngineConfig and ConfigResolver.
- Add Catch2 test coverage and verify BEIR scifact benchmark metrics.
Signed-off-by: trvon <me@trevon.dev>
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trvon
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052031a484
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feat(vector): binary quantization (BQ) pre-filter for cluster routing
- Add BinaryQuantizer and BinaryQuantizedIndex in include/yams/vector/binary_quantization.h and src/vector/binary_quantization.cpp implementing 1-bit sign quantization, packed 64-bit word storage, hardware popcount Hamming distance, and cosine similarity estimation. - Integrate centroidBqIndex into SparseRouteIndex, constructing compact BQ centroids alongside dense ANN indices during SparseGuidedClusterRouter::buildRouteIndex. - Add bqCandidateLimit to TopologyRouteRequest and tracking metrics (bqUsed, bqCandidates, bqDistanceEvaluations) to SparseRouteWork. - Enable fast candidate pre-filtering in SparseGuidedClusterRouter::route with 1-bit Hamming distance scans, providing sub-millisecond coarse candidate shortlisting and automatic fallback when the dense ANN index is omitted. - Add Catch2 unit test suites in tests/unit/vector/binary_quantization_catch2_test.cpp and tests/unit/topology/topology_baseline_catch2_test.cpp. Signed-off-by: trvon <me@trevon.dev> |
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trvon
|
dd8105f25d
|
perf(topology): bypass metadata table triggers during snapshot sync and prune legacy metadata
- Add Migration 41 to drop and recreate metadata_value_counts triggers with 'WHEN ... AND key NOT LIKE topology.%' condition, eliminating ~650,000 trigger executions per topology rebuild in a 72k document corpus. - Purge legacy continuous float/structural keys from metadata table (persistence_score, cohesion_score, bridge_score, role, cluster_level, parent_cluster_id, overlap_cluster_ids_json) in Migration 41. - In MetadataKgTopologyArtifactStore::storeBatch, replace N individual getDocumentByHash calls with single batchGetDocumentsByHash and write only essential snapshot_id and cluster_id to metadata table. - In MetadataKgTopologyArtifactStore::loadMemberships, add in-memory fast path serving memberships directly from cached latest snapshot batch. - Update serializeTopologyBatchCompressed to handle uncompressed tiny batches. - Add Catch2 unit tests in tests/unit/topology/topology_metadata_store_catch2_test.cpp validating trigger bypass, metadata pruning, and fast-path membership loading. Signed-off-by: trvon <me@trevon.dev> |
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|
trvon
|
8fdb4df27e
|
feat(topology): binary snapshot serialization and zstd compression
Replace 960+ MB raw JSON snapshot serialization in MetadataKgTopologyArtifactStore with a compact, string-interned binary format compressed with Zstandard. - Add yams::topology::serializeTopologyBatchBinary and deserializeTopologyBatchBinary with integer length packing and string deduplication. - Wrap binary payload in a backward-compatible JSON envelope with format: zstd_binary_v1 and base64 encoded payload, maintaining SQLite json_valid(properties) == 1. - Fall back gracefully to legacy raw JSON deserializer when reading pre-existing uncompressed snapshots. - Add Catch2 unit test suite verifying binary roundtrip fidelity, compression ratio, backward-compatibility with legacy JSON snapshots, and corrupted payload resilience. Signed-off-by: trvon <me@trevon.dev> |
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|
trvon
|
745818e67d
|
perf(topology): streamline artifact construction
Reuse admitted relations and dense splitter state while preserving deterministic identities, centroids, and the 64-document safety cap. Add corpus-shaped benchmarks so construction regressions stay measurable. |
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Trevon
|
3f37e8f564 |
Sync experimental into main: Search retrieval improvements (#60)
* fix(graph): handle qualified C++ symbols Signed-off-by: trvon <me@trevon.dev> * refactor(vector)!: remove dead transition APIs Split Simeon vector and retrieval linkage so consumers inherit only the runtime surface they use. BREAKING CHANGE: remove unused async/model/config helpers and the undefined vector-backend factory from public headers. Signed-off-by: trvon <me@trevon.dev> * fix(vector): harden PQ snapshot lifecycle Validate and atomically install persisted generations, revalidate after races, and fall back to exact search when a snapshot is stale. Add the exact-scan reference lane and distinguish observed work counters from unavailable backend metrics. Signed-off-by: trvon <me@trevon.dev> * feat(topology): expose route coordinates Persist chart distortion and local-dimension evidence, retain pre-scalarization route axes, and emit detailed trace rows without treating unavailable vector work as zero. Signed-off-by: trvon <me@trevon.dev> * feat(xplan): add vector decision gates Track binary and corpus identity, preserve missing-work semantics, and add repeated PQ routing, crossover, and rerank plans with quality and cost summaries. Signed-off-by: trvon <me@trevon.dev> * feat(topology): formalize coordinate routing Separate chart geometry from route-risk admission and prove candidate-stage recall and strict-focus boundaries. Record the measured atlas limitations and literature basis for the next construction experiment. Signed-off-by: trvon <me@trevon.dev> * fix(search): serialize SymSpell readers SQLite-backed lookups reuse mutable prepared statements, so shared-reader locking is unsafe. Advance the owned SymSpell revision for batched delete insertion and cover concurrent root lookups under TSAN. Signed-off-by: trvon <me@trevon.dev> * fix(vector): make mutations atomic Preserve stored vectors on replacement and commit failures, reject cross-thread writes during explicit transactions, and restore exact reranking for quantized-primary PQ rows. * fix(search)!: surface SymSpell write errors Propagate persistent dictionary failures through metadata ingestion, roll back failed batches, and make clear remove stored terms. BREAKING CHANGE: SymSpellSearch mutations now return Result values. * feat(topology): formalize candidate expansion * feat(vector): add coordinate-aware embeddings * feat(topology): preserve protected relation cover * feat(search): add graph candidate rescue * feat(daemon): expose retrieval hydration telemetry * feat(xplan): add rescue and hydration gates * refactor(content): dedupe media handlers Reuse shared graph presenter helpers and centralize repeated audio/video/archive buffer processing, validation, lifecycle, and stats helper logic. * feat(lifecycle): prune stale corpus data Keep cleanup preview-first while retention stays opt-in and long prune work no longer holds IPC responses open. * feat(search): add topology candidate rescue Preserve high-value routed candidates across vector backends while keeping exact rerank diagnostics explicit. * feat(search): expose evidence paths * docs: define mobile host contract * formal: model bounded candidate rescue * fix(prune): inspect extensionless signatures * fix(prune): tolerate stale extensions --------- Signed-off-by: trvon <me@trevon.dev> |
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|
Trevon
|
7df64b1161 |
perf(search): bound topology routing and harden runtime paths (#59)
* fix: address review build issues * perf(search): bound topology routing Cache route membership, shortlist centroids with static ANN, and route SPQ through explicit allowed-document budgets. * test(xplan): measure routed vector work Pin benchmark binary identity and export route, cache, and phase costs for repeated equal-budget comparisons. * test(search): use portable jthread wrapper * fix(daemon): serialize detached cancellation * fix(cli): honor pinned daemon sockets * fix(xplan): support Windows contract imports * fix(list): apply metadata filters before paging * docs(prompts): require memory hydration Treat search results as candidates and hydrate selected artifacts before use. Quote argument hints for strict YAML loaders. * test(cli): keep add on pinned daemon * test(metadata): isolate performance timing * fix(graph): tolerate stale snippet ranges Source files may change before persisted symbol metadata is refreshed. Omit stale snippets instead of aborting graph exploration. * test(daemon): await request readiness Reuse the retrying list probe before asserting post-shutdown error quality under sanitizer load. * ci(release): use hosted cmake Resolve Conan CMake tool requirements from PATH so cold ARM64 caches do not depend on cmake.org. Default BUILD_DIR for failure cleanup. |
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|
Trevon
|
a3d065dd8d |
feat(search): make topology-assisted retrieval the default (#57)
* fix(release): repair package repo publish
Arch repo metadata and R2 uploads need to be reproducible from CI, with retry hardening for transient Cloudflare failures.
* fix(daemon): stop shutdown log storm
Init waiter must treat ShuttingDown as terminal so daemon shutdown tests do not flood Meson logs while the daemon is stopping.
* refactor(cli): delegate serve to MCP binary
Keep yams serve UX while removing MCP server linkage from yams-cli. The standalone MCP binary owns stdio serving and exits on stdin EOF.
* refactor(cli): move daemon path helpers
Keep CLI path resolution out of YamsDaemon so later link cuts can separate CLI and daemon internals. Full yams_daemon removal still needs a socket-only daemon-client split.
* refactor(daemon): split embedded client
* perf(search): add lean-guided benchmark gates
Add Lean topology/search models, ingestion ablation docs, and focused regression tests for topology and compression threshold behavior.
Extract search observability, keep benchmark-only ablation controls, and make retrieval quality benchmarks default to Simeon while preserving explicit ONNX opt-in.
* refactor(config): move daemon policies
* refactor(daemon): extract plugin runtime
* refactor(daemon): untangle service coordinators
Untangle CLI/MCP from daemon service coordinators and the daemon static lib.
- MetadataRepository uses a daemon-neutral tree-diff callback. The
GraphComponent wrapper moves to src/daemon/components/metadata_graph_bridge.cpp,
owned by the daemon library.
- WriteCoordinator moves to a dedicated build-only yams_write_coordinator
static lib. Drop ResourceGovernor coupling inside the writer loop; batch
sizing still respects config.maxBatchSize.
- AppContext gains enqueuePostIngest callback. ServiceManager wires it to
its own enqueuePostIngest; app services no longer call ServiceManager
directly.
- Embedding repair uses BulkIngestLease/BeginBulkIngestCallback instead of
concrete VectorIndexCoordinator::BulkScope. Daemon dispatchers provide a
lease factory backed by the real coordinator.
- CLI daemon_command uses config helpers instead of YamsDaemon::getXDGRuntimeDir.
- Remove explicit dependency('yams_daemon') from src/cli and tools/yams-mcp.
- Declare missing yams_extraction/yams_ingest deps on yams_app_services so
app services link cleanly without daemon.
Validated:
meson compile -C build/release -j4 yams-daemon yams-cli yams-mcp-server
ninja -C build/release -t commands tools/yams-cli/yams-cli tools/yams-mcp/yams-mcp-server | grep -c libyams_daemon.a -> 0
yams-cli --version, yams-mcp-server init, yams serve --help smoke tests
Size drop on macOS release: yams-cli 41M -> 32M, yams-mcp-server 37M -> 22M.
* fix(cli): keep stdin add local fallback
No embedded daemon now. When yams add - buffers stdin and daemon IPC is missing, store via local app services instead of failing socket_missing.
Validated:
meson compile -C build/debug -j4 yams-cli catch2_cli_commands
MESON_BUILD_ROOT=/Users/trevon/work/tools/yams/build/debug build/debug/tests/catch2_cli_commands 'AddCommand - reads from piped stdin and stores content'
MESON_BUILD_ROOT=/Users/trevon/work/tools/yams/build/debug build/debug/tests/catch2_cli_commands
meson compile -C build/release -j4 yams-cli yams-mcp-server
meson compile -C build/asan-api -j2 yams-cli catch2_cli_commands
MESON_BUILD_ROOT=/Users/trevon/work/tools/yams/build/asan-api ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 build/asan-api/tests/catch2_cli_commands 'AddCommand - reads from piped stdin and stores content'
ninja -C build/release -t commands tools/yams-cli/yams-cli tools/yams-mcp/yams-mcp-server | grep libyams_daemon.a -> no output
* feat(bench): add xplan multi-arm experiment harness
Unified plan runner, ablation axes, REPORT/ablation docs, and
KPI snapshot so optimization loops stop living in shell matrices.
* feat(formal): expand topology/search Lean contracts
Boundary models for search provenance, construction gates,
and cluster/route objectives so Lean guides correctness while
xplan ranks performance levers.
* feat(search,topology): construction purity + graph expansion path
Raise topology build defaults (min edge 0.25, max component 64) and
split oversized CC pieces so hybrid assist is quality-positive on
scifact. Add GraphNeighbors expansion with medoid-anchor fallback,
structured helpers instead of nested session logic, and BEIR-default
xplan plans. Search engine extraction (fanout/classic pipeline) rides
along as the integration surface for routing.
* feat(topology): add KMeans engine and SGC identity contracts
Register kmeans in the factory with deterministic spherical k-means
over embeddings, and enforce SGC document-identity invariants in
debug builds with matching unit coverage.
* feat(daemon): topology readiness gates and selectable reranker
Drive topologyReady from published epoch/freshness/rebuild/dirty
ingest state (not just KG drain), surface those fields in search
stats, and wire onnx|simeon|auto|none cross-reranker selection.
* chore(search): drop meta_path tuner knobs
Meta-path routing is gone; remove dead TunedParams fields and the
ConfigResolver test for [search.meta_path].
* feat(bench): add topology_purity_validate plan
Repeats=3 validation matrix for construction-purity winners vs
topo_off so MRR deltas can clear run-to-run noise.
* chore: format add_command and config include order
Mechanical clang-format / include reorder only; no behavior change.
* feat(bench): decision-grade xplan loop for search engine
Document search-engine measurement in AGENTS; harden xplan with
repeats=3 plans, quality×latency primaries, mechanism metrics from
debug.jsonl, multi-rep log promotion, and archive superseded topology
plans.
* feat(graph): denser product semantic_neighbor topK
Raise default YAMS_GRAPH_SEMANTIC_TOPK fallback from 4 to 8 so product
graphs leave fewer degree-0 docs for GraphNeighbors expansion.
* feat(search): extract topology assist and cross-rerank seams
Pull topology assist into search_topology_stage (seed merge, skip
reasons, optional vector seed probe default 0). Extract cross_rerank
compute from search_engine. Wire probe via typed config/ConfigResolver.
* feat(bench): product-path search engine ablation plans
Add topology-off component, vector-weight, and tiered-execution xplan
plans (repeats=3) and wire them into the AGENTS measurement loop table.
* fix(ci): repair pre-push fallbacks
* feat(bench): lock-free mid-run builds + multi-corpus gates
xplan skips meson rebuild when the quality binary exists (flock +
YAMS_BENCH_FORCE_BUILD override) to stop multi-arm link races. Add
graph_vector weight and nfcorpus transfer-gate plans; document in AGENTS.
* fix(daemon): keep SearchEngine alive via shared_ptr cache
getCachedEngine previously published a raw pointer that metrics polling
used through rebuild, racing destructor of SearchEngine::Impl (TSAN).
Store and return a shared_ptr snapshot so diagnostic readers pin the
engine for the duration of getConfig/health checks.
Also adds the cautious vectorWeight 0.30→0.20 multi-corpus xplan plan.
* feat(search): route vectors through cached topology
Build and reuse validated topology snapshots, rank routed members by query similarity, and narrow the vector leg to the accepted document set with explicit work diagnostics.
Remove the retired HDBSCAN engine and vendor dependency, preserve typed topology policy through search tuning, and cover the runtime/configuration contracts.
* feat(bench): consolidate search decision plans
Enforce deterministic experiment identity and declared baselines, expose routed/global vector work metrics, and register the focused benchmark contracts.
Promote the compact repeats=3 routing-budget gate, archive superseded topology mechanism screens, and add multi-corpus product calibration plans.
* feat(search): refine topology vector routing
* fix(search): propagate daemon readiness
* feat(bench): measure generalized memory health
* fix(cli): honor in-process fallbacks
* ci: harden smolvm debug builds
* perf(search): route topology through filtered ANN
* feat(bench): measure read-write pressure
* perf(metadata): index symbol lookups on read pool
* fix(daemon): isolate startup reads and maintenance
* feat(bench): replay isolated generalized corpora
* feat(search): add evidence routing pipeline
Replace the blocking smolvm pre-push path with host ASan/TSan validation, harden sanitizer-sensitive smoke tests, and add recovery cleanup for malformed SQLite WAL sidecars.
* refactor(search): unify topology evidence path
Remove classic and sidecar fusion lanes so topology augments the recall-preserving ANN and lexical candidate pool through one product path.
* refactor(bench): prune superseded search lanes
Measure the topology-plus-ANN product path with stable experiment identity and remove obsolete sidecar and tiered controls.
* docs(search): retire stale experiment notes
Keep the benchmark handoff focused on the topology-plus-ANN product lane and its active decision plans.
* refactor(search): prune dead search surfaces
Remove unused fusion, reranker, policy, and router abstractions.
Bound topology materialization and keep document trace payloads opt-in.
* fix(cli): clear build warnings
* fix(xplan): reject stale run identity
* refactor(search)!: remove legacy query stack
Replace the unused AST/ranker/post-processor surface with focused facet aggregation used by product search.
BREAKING CHANGE: removes query parser, result ranker, search filter, and SearchResults container APIs from yams_search.
* refactor(search): type value stage traces
Remove synthetic ComponentResult markers for embedding and concept stages. Preserve failure and timeout states instead of overwriting them with fake successful results.
* refactor(search): isolate benchmark env overlays
Move test-only search environment parsing behind an injectable internal adapter. Keep all existing overlay keys and tuner pin semantics while restoring SearchEngineBuilder to composition.
* refactor(search): unify topology routing options
Snapshot topology policy once at the assist boundary and pass it through routing sessions and diagnostics. Remove repeated scalar copying without changing routing behavior or metric keys.
* fix(search): unify tuner config ownership
Use one complete config-to-params overlay for runtime seeding and no-tuner policy resolution. Reseed attached tuners on setConfig so reported and executed configuration cannot diverge.
* fix(search): snapshot tuner state per query
Read tuned config, params, and state under one lock before routing. Add a TSAN correlation test so adaptive observation cannot produce a torn logical query snapshot.
* fix(search): enforce topology routing contract
Generated configs must preserve hybrid-assist shadow routing, while daemon-backed search must abstain when published topology artifacts are stale. Keep standalone validation and global ANN recall intact.
* fix(daemon): let SQLite reclaim its file
Directly resizing a live database from sampled page counts can truncate pages allocated by concurrent writers. VACUUM must remain the only file-reclamation mechanism.
* fix(metadata): tolerate missing symbol FTS
Readiness lookups can race an unavailable optional FTS migration. Retain the indexed fast path, but retry against the base table when prepare or cached-statement execution proves the capability absent.
* build(fuzz): drop removed query parser target
The optional AFL build still referenced the deleted legacy query parser API and could no longer compile.
* fix(bench): include writes in drain oracle
A zero post-ingest queue is not durable drain while coordinated writes remain queued or in flight.
* fix(daemon): vacuum padded WAL databases safely
|
||
|
Trevon
|
bfe7cd94ca |
test: expand storage-readiness coverage — 48.1%→59.8% broad, 74.3% narrow (#38)
* fix(daemon): avoid socket cancel on stop Signal active sockets with shutdown only so pending I/O wakes without entering Boost.Asio's reactor cancel path during teardown. * fix(metadata): open read pools read-only * ci: fix coverage report generation * fix(metadata): tag unscoped pool holders * test(daemon): avoid ipc teardown takeover * ci: skip plugin coverage objects * fix(daemon): repair completed FTS5 ghosts * build(vector): guard unusable FAISS headers * ci: use clang gcov for coverage * test(daemon): stabilize arm CI flakes * Harden search and compression numeric config * fix(daemon): reconcile orphan vector embeddings * fix: address vector cleanup review comments * chore(main): release 0.16.1 * Harden search ranking divisors * Harden snippet distance and command registration * test(storage): add readiness coverage gate Document the distributed sync readiness surface and add direct adapter, refcount, and GC failure-path coverage. * test(storage): cover strict resolver fallback * fix(search): tighten retrieval ranking Honor component weights in default RRF, over-fetch vector chunks before document aggregation, and persist topology centroids for sparse-guided routing. * fix(search): route weak queries through topology * fix(search): improve rerank and weak queries Wire provider-backed cross reranking, add direct Simeon candidates for weak lexical pools, and report stage-level retrieval metrics. * fix(storage): honor explicit plugin names Add readiness coverage for factory, URL backend, and compressed storage failure paths. * fix(storage): avoid remote size listing * fix(api): rollback failed content adds * test(storage): cover engine readiness * test(storage): cover compressed readiness * fix(core): harden delete and recovery paths Route prune and local delete fallback through DocumentService so content, metadata, vectors, and KG cleanup stay consistent. Treat transient SQLite quick_check lock failures as ResourceBusy, refresh IPC activity on streaming writes, and preserve reranker config in tuner seeding. * test(storage): cover URL backend readiness * fix(api): harden content rollback * feat(storage): add list seam, URL listing, and write-edge coverage * feat(api): reconcile ambiguous remote manifest writes * feat(storage): add deep compressed scan validation * test(storage): add plugin loader error path coverage * fix(gc): prune reference rows after collection * test(api,storage): add health, compact, gc, and verify edge coverage * docs: update storage-readiness coverage to 71.8% * test(metadata): add connection pool shutdown-while-leased coverage * test(metadata): add tree builder snapshot root stability coverage * test(vector): add before-init and after-close operation rejection coverage * test(metadata): add database post-close, open-failure, and cache-clear coverage * test(integrity): add P2P wrong-hash rejection + batch matrix resolution * docs: audit and resolve all matrix rows — 18 fully covered * test(metadata): add failed-migration and rollback coverage * test(storage): add getBlockSize-invalid-key, empty-verify, PUT/DELETE retry coverage * feat(storage): add file-open and rename failure hooks + ContentStore retrieve edge coverage * docs: add broad-surface coverage with per-subsystem breakdown * test(integrity): add chunk validator manifest validation coverage * test(vector): add batch insert, delete, and update operation coverage * docs: update integrity subsystem coverage to 46.4% * docs: consolidate coverage report — clean matrix, remove boilerplate * docs: update coverage with complete-suite numbers — 59.8% broad, 74.3% narrow * test(storage): add URLBackend HEAD exists with 2xx coverage * bump submodules * fix: address PR review — curl_slist leak, ec ordering, CAS rollback, production hooks --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> |
||
|
Trevon
|
9c8f51b673 |
refactor(daemon): write-architecture — WriteBatchCoalescer, MetadataWriteFacade, tryEnqueue, batch coalescing (#28)
* feat: search work and moving to experimental
* WIP
* feat(search): diagnostic logging pipeline — graph build, concepts, reranker gate
- New [concepts] per-50-query log showing extracted query concepts, type
distribution, and used_gliner flag.
- New [PIQ-entity] per-1000-dispatch + per-document completion log with
entity type counts (e.g., 'protein=3, gene=1, chemical=2').
- New [graph_rerank-gate] one-shot log showing why enableGraphRerank
is zeroed: shows shortQueryBudgeted, corpusWarming, bypassWarmingGate,
lexicalReady, and post-ingest inflight.
- New [graph_rerank] per-50-query log with window size, matched
candidates, applied count, concept count, and elapsed time.
- retrieval_quality_bench.cpp: add YAMS_SEARCH_BYPASS_CORPUS_WARMING_GATE=1
so benchmark queries are not gated by freshness checks.
- resolve merge conflicts from experimental branch.
* fix(search): enable entity extraction for text files via GLiNER fallback
- prepareMetadataEntry: shouldDispatchEntity now also checks hasTitleExtractor()
so plain-text files (.txt, .md) get entity extraction even when no binary
entity provider supports their extension.
- processEntityExtractionStage: when no ExternalEntityProvider matches,
fall back to processTitleExtractionStage which runs GLiNER on text.
- refreshStageAvailability: entity stage is now considered capable when
hasTitleExtractor() is true, so the entity poller gets concurrency budget
even if entityProviders_ is empty.
- kCombinedEntityTypes: add biomedical entity types (protein, gene, cell,
disease, chemical, drug, pathway, biological_process, biomarker, anatomy,
organism) so GLiNER extracts high-value biomedical entities instead of
only generic NL types (person, organization, concept).
* perf(bench): add YAMS_POST_ENTITY_CONCURRENT=4 for text entity fallback throughput
* feat(search): fast token-based entity extraction for text documents
- Replace slow GLiNER-based entity extraction (~260ms/doc) with fast
token-based concept mining (~1ms/doc) via generateFallbackQueryConcepts.
Uses sub-phrase mining + IDF-weighted token salience — the same function
already used for query-time concept fallback.
- Store entities with full KG scaffolding: KGNode with entity type/label,
KGAlias for query-time resolution, DeferredEdge from entity→document,
and DeferredDocEntity linking entity to document for getDocEntitiesForDocument.
- Add biomedical entity types to kCombinedEntityTypes in title extraction
(protein, gene, cell, disease, chemical, drug, pathway, etc.) so GLiNER
can output high-value biomedical entities when used.
- Add include for query_expansion.h to access generateFallbackQueryConcepts.
- bench: add YAMS_POST_ENTITY_CONCURRENT=4 for entity poller throughput.
Benchmark: 22K+ entities extracted across 5183 docs, ~41% high-value
biomedical. MRR 0.4281 (beats 0.4273 baseline by +0.2%).
* feat(diag): add firstDocEntities check to graph_rerank-gate log
- Queries kg_doc_entities for the first candidate document to verify
whether fast entity writes were committed before queries start.
- Confirmed: firstDocEntities=0 — entities stuck in WriteCoordinator
async queue when benchmark queries begin.
* fix(search): add periodic write-coordinator flush during entity extraction
Entity writes enqueued via writeCoordinator_ can accumulate since the
writer loop is capped at 8 batches/iteration. For 5K+ documents this
creates a backlog that outlasts the post-ingest drain wait — entities
are not committed to kg_doc_entities before benchmark queries start.
Add a periodic flush (every 128 batches, 500ms timeout) in the entity
extraction batch processor to drain the WC queue incrementally.
Diagnostic confirms firstDocEntities=0 persists — a synchronous
committed flush or batched WC enqueue is needed.
* fix(docker): add gfortran for openblas arm64 build
* fix(search): accumulate entity writes into shared WC batch, flush once
The WriteCoordinator writer loop is capped at 8 batches/iteration. With
5K+ per-doc entity writes, entities outlast the benchmark's post-ingest
drain and firstDocEntities=0 when the graph scorer runs.
- processEntityExtractionStage: add optional DeferredKGBatch* parameter.
Text-fallback appends entity nodes/aliases/edges/doc-entities to the
shared batch instead of creating per-doc WC batches.
- processEntityExtractionBatch: creates one DeferredKGBatch, passes it to
all stage calls in the batch, enqueues to WC once at end.
- Single-shot WC flush: after all stages go idle (totalInFlight==0),
calls writeCoordinator_->flush(15s) to drain remaining entity writes
before benchmark queries start.
- DeferredKGBatch forward-declared in PostIngestQueue header.
* ci: fix free-disk-space action ref, sha didnt exist
* fix(search): revert WC accumulation, fix text fallback to per-doc writes
The shared-batch WC accumulation approach worked conceptually but:
- WC flush with totalInFlight==0 fires too early (before last batch)
- generateFallbackQueryConcepts produces empty concepts for 99% of
document texts (designed for short queries, not abstracts)
- Only 1/5183 docs produced concepts → 1 doc worth of entities in KG
Revert to simple per-doc entity extraction. The enable=/disable=
graph reranker gate is still controlled by shortQueryBudgeted=1
which zeroes the graph reranker on the first query (intent=Code).
firstDocEntities=0 persists — entities need a different creation
strategy for document text (phrase mining too conservative).
* fix(docker): add curl retry for Zig download
* feat(search): per-profile ConceptExtractionBackend (Fallback vs GlinerWithFallback)
- search_engine_config.h: new ConceptExtractionBackend enum with Fallback
(sub-phrase mining + IDF tokens, <1ms) and GlinerWithFallback (GLiNER
first, fall back on empty/timeout). Default: GlinerWithFallback.
- search_tuner.h: SCIENTIFIC profile sets Fallback (GLiNER returns empty
for 99% of short biomedical claims). Other profiles keep default.
Wired through TunedParams.applyTo().
- search_engine.cpp: gate GLiNER concept extraction on the config backend.
When Fallback, conceptFuture is never created and concepts come directly
from generateFallbackQueryConcepts. Added [concept-backend] diagnostic.
- search_engine_builder.cpp: builder log now includes concept_backend
in the override-state startup message.
- search_tuner_catch2_test.cpp: verify SCIENTIFIC profile uses Fallback.
Note: builder correctly sets Fallback but query-time workingConfig still
shows GlinerWithFallback (int=1). This is a config-sync issue between
builder-time profile application and runtime config snapshot — the
tuner or a post-override config copy may reset the field. To be fixed.
* refactor(search): extract concept resolver, per-profile backend, clean dead code
- New concept_resolver.h/cpp: extract enrichWithFallbackConcepts from the
search engine monolith into a testable unit. Generates IDF-weighted
token concepts via generateFallbackQueryConcepts, deduplicates, and
appends to existing concepts.
- search_engine_config.h: new ConceptExtractionBackend enum (Fallback vs
GlinerWithFallback). SCIENTIFIC profile sets Fallback since GLiNER
extracts 0 concepts for 99% of short biomedical claims.
- search_tuner.h: wire conceptExtractionBackend through TunedParams,
applyTo, seedTunedParamsFromConfig (the one-line fix that resolved
the config-sync bug where profile Fallback was overridden at query
policy resolution time).
- search_engine.cpp: materializeConcepts lambda restructured to always
reach the fallback even when GLiNER future is invalid. Removed
~80 lines of diagnostic bloat ([concept-backend], [workingConfig-*],
per-50 [concepts]). GLiNER gate checks config backend.
- PostIngestQueue.cpp: removed dead fast-token entity extraction
(~150 lines of concept generation + KG scaffolding that produced
0 entities for 99% of documents). Reverted entity-stage gating
(entityCapable || hasTitleExtractor) and shouldDispatchEntity to
extension-only checks. Removed DeferredKGBatch forward decl.
- gliner_query_extractor: removed unused createGlinerExtractionFunc-
FromProvider fallback factory (~150 lines).
- ServiceManager.cpp: removed fallback call site for removed factory.
- builder log: removed concept_backend diagnostic line noise.
- search_tuner_catch2_test.cpp: verify SCIENTIFIC uses Fallback.
Net: ~400 lines removed, ~120 lines added (concept_resolver unit +
config wiring). GLiNER concept extraction savings: ~30-80ms/query
× 300 queries = 9-24s total for SCIENTIFIC profiles.
* fix: entity stage only for binaries, title stage for text
entity stage = binary providers (Ghidra/Zyp). title stage = GLiNER for all
text. No overlap — title already stores NL entities to KG.
* fix(docker): add wget for Zig, disable faiss
openblas arm64 build fails in Docker containers. YAMS_DISABLE_FAISS=1
env var skips faiss (and its openblas transitive dep). Zig download
now uses wget -c for resume on flaky ziglang.org connections.
* ci: add experimental branch to tests trigger
* ci: pin free-disk-space to v1.3.1
* feat: Simeon concept mining entity export for graph reranker
- simeon_lexical_backend.h: EntityCallback in Config. Called with
(docId, entityText, confidence) per concept match per doc.
- simeon_lexical_backend.cpp: after mine_concepts, iterate docs
via collect_doc_concepts + entity_callback.
- SearchEngineManager.cpp: enable concept_mining_enabled, wire
entity_callback batch-inserting DocEntity via KG store. Fix
kgStore capture-before-move race.
Note: simeon submodule has collect_doc_concepts in concept_mining.hpp
+ concept_mining.cpp (must commit to submodule separately).
* ci: disable faiss in warm and test jobs
* ci(bench): add faiss disable, ccache, and failure diagnostics to weekly benchmarks
* fix(metadata): retry constraint failures in executeQueryOnPool
FK race on Linux causes transient constraint failures when metadata
write races ahead of document commit. Previously treated as terminal.
Now retried with backoff like lock errors.
* fix(metadata): deduplicate batch entries before UPSERT
Duplicate (document_id, key) pairs within a single batch cause SQLite
ON CONFLICT DO UPDATE to fail with constraint violation. Dedup keeps
the last write per key.
* chore: bump simeon, add extraction readiness stats
Simeon: 8bf225e -> 6320ab6 (adapter + QPP router framework).
CorpusStats: add contentExtracted*, ftsIndexed*, titleCoverage,
languageCoverage, and KG topology richness fields.
* feat(search): integrate simeon EntropyRouter strategy lane, corpus-state tuning
- Wire EntropyRouter + Keyphrase/LeadField strategies into SimeonLexicalBackend
- Add scoreStrategyRouted(), hasStrategyRouter(), strategy_router_enabled config
- Add YAMS_SIMEON_STRATEGY_ROUTER_ENABLED env wiring
- Add applyCorpusStateAdjustments(): per-corpus-state recall push (vec max,
rescue slots, weak-query fanout, entity vec expansion, NER damping)
- Extend CorpusStats with extraction/FTS/title/language/KG edge+alias density
- Add hasRichGraphTopology(), nerOnlyNoEdges damping to graph adjustments
- Add 14 new engine-policy benchmark candidates (retrieval lanes, RRF sweep,
aggressive recall, strategy router)
- Weight miss_pre_fusion_rate in optimization objective (0.25x)
- Add Simeon lexical concept/doc count to IndexFreshnessSnapshot + status
- Bump simeon submodule (retrieval_strategy + corpus_adapter API)
* feat(search): add concept_count and concept_mining_enabled accessors
* feat(search): add ScientificAdapter + RM3 PRF blend
ScientificAdapter: training-free entity extraction for scientific
text via regex/suffix patterns (biomedical suffixes, ALL_CAPS symbols,
capitalized multi-word terms, measurements). Replaces TextAdapter
in strategy router build, providing entity lists for KeyphraseStrategy.
RM3: add score_with_prf blend path to scoreStrategyRouted at 0.30
weight when rm3_enabled=true. New benchmark candidate
scientific_strategy_rm3.
Strategy router + ScientificAdapter: mrr=0.4514 ndcg=0.4789 recall=0.5849
* docs: soften governance and contribution prose
Replace prescriptive language ('must', 'require', 'adjudicates') with
friendlier, more welcoming phrasing across governance docs, PR template,
security policy, and contributing guide.
* feat(extract): add language-agnostic IMRAD section detection, expand entity types
detectDocumentSections(): structural heuristics for title/abstract/body
using line-length, ALL_CAPS, numbering patterns. No word matching.
Works across all languages and scripts.
deriveTitle(): add IMRAD detection step before first-line fallback.
isHighValueGraphType(): use ScientificAdapter suffix detection (40+
biomedical suffixes) instead of hardcoded 11 types.
* feat(ingest): field-weighted FTS5, IMRAD claim segmentation, ScientificAdapter fallback
- FTS5: title tokens repeated 3x, abstract 2x, body 1x in content
field for BM25 field weighting without schema migration
- IMRAD-aware claim segmentation: buildBodyClaimSegments splits
each detected section independently, distributes maxSegments
- ScientificAdapter fallback: when GLiNER unavailable, inline
entity extraction via suffix/pattern detection → direct KG write
- Add abstract field to PreparedMetadataEntry + BatchContentEntry
* refactor(daemon): extract enrichment stages to post_ingest_enrichment.cpp
Split PostIngestQueue.cpp (3145 lines) into:
- PostIngestQueue.cpp (~3084 lines): coordinator, lifecycle, queue
management, extraction pipeline, gradient limiters
- post_ingest_enrichment.cpp (new, 701 lines): KG/symbol/entity/title
stage processing with self-contained enrichment utilities
* fix(daemon): restore enrichment utilities to PostIngestQueue.cpp
Processing methods still in PostIngestQueue.cpp reference entity/NL
utilities (isUsefulNlEntity, buildBodyClaimSegments, etc.) that were
removed during decomposition. Restore them to anonymous namespace.
* fix: address PR #25 Copilot review feedback
- Add missing #include <unordered_map> to concept_resolver.cpp
- Batch entity writes per doc in SearchEngineManager (reduces write amp)
- Remove non-existent CorpusAdapter API claims from README
- Replace absolute paths with repo-relative in daemon-download-jobs.md
- Revert plugin-zyp default to false (noisy warnings)
- Fix grammar in extraction-repair-pipeline.md heading
- Add gitignore entries for .wrangler, .claude, .artifacts, papers
* fix: Copilot feedback - IDF passthrough, batch flush, debug gate, IMRAD comment
- Pass IDF map through enrichWithFallbackConcepts for weighted fallback
- Batch entity writes per doc with threshold flush in SearchEngineManager
- Downgrade graph_rerank-gate diagnostic to spdlog::debug
- Add TODO for entity_callback wiring during concept mining
- Fix DocumentSections comment to match language-agnostic implementation
* chore: bump simeon (ScientificAdapter v3)
* fix: resolve merge conflict markers, add missing <random> include
Remove leftover <<<<<<< / ======= / >>>>>>> from earlier merge.
Add #include <random> to ingestion_throughput_bench.cpp.
* chore: trigger CI after simeon submodule push
* perf(daemon): event-driven topology rebuild — replace timer with post+re-enter
When pipeline isn't drained, instead of breaking out of the rebuild
loop (and losing the rebuild opportunity), re-post via requestTopologyRebuild.
This yields to poller work on the executor before retrying, providing
natural event-driven coalescing without timers.
Combined with publishing topology_artifacts_fresh to readinessStates
and the benchmark's search probe loop, this achieves:
- Simeon throughput: 0.6 → 11.4 docs/s (19x)
- Keyword-searchable: 512ms → 144ms (3.5x)
- Hybrid-searchable: 1024ms → 260ms (4x)
- Searchable gate passes for the first time
* feat(kg): add edge/alias atomic counters for online overlay stats
- Add edgeCount_/aliasCount_ atomics to SqliteKnowledgeGraphStore
- Track edge/alias deltas in SqliteWriteBatch (addEdgesUnique/addAliases)
- Initialize from DB at startup (initializeEntityCountSnapshot)
- Surface in KGEntityCountSnapshot → getCorpusStats overlay merge
- Enables hasRichGraphTopology() in overlay mode, making entity vector
and graph rerank activation immediate instead of requiring full reconcile
* fix(kg): wire entity/edge/alias atomics for real-time overlay stats
- Add updateEnqueueCounts() virtual to KnowledgeGraphStore
- SqliteKnowledgeGraphStore increments edge/alias atomics immediately
- Call from processTitleExtractionStage + ScientificAdapter fallback
- getCorpusStats overlay merge reads edge/alias from snapshot
- Benchmark: skip ONNX preferred_model when simeon backend active
* fix(daemon): flush WriteCoordinator before drain signal
checkDrainAndSignal now calls writeCoordinator_->flush(30s timeout)
before signaling corpus stats stale. Ensures all entity/edge/alias
batches are committed to DB before the search engine rebuild reads
overlay stats. Fixes the timing gap where the rebuild fired before
GLiNER title extraction data landed.
* fix(daemon): suppress unsupported-symbol noise, auto-trust benchmark plugins
- EntityGraphService: rc=-2 extract_symbols downgraded from warn to debug;
unsupported languages memoized via lazy-init cache to skip future
attempts; skip DB write for rc=-2 failures to reduce WriteCoordinator
contention
- WriteCoordinator: silently skip UpsertSymbolExtractionStateOp on
database-is-locked (expected under load, not actionable)
- Benchmark harness: auto-trust /opt/homebrew/lib/yams/plugins and
/usr/local/lib/yams/plugins so GLiNER title+NL extraction loads in
Simeon benchmark runs
Result: extract_symbols log noise eliminated, title stage active (49/59
consumed in Simeon profile), benchmark throughput stable at 12.99 docs/s
* perf(daemon): event-driven search build + non-blocking corpus stats
- SearchEngineManager: replace timer-race build with event-driven completion.
Build posts to worker and completes when work finishes. 300s hang guard
replaces aggressive 5s/30s timeout that was causing false failures.
- search_engine_builder: skip getCorpusStats() on build critical path for
non-empty corpora — use default tuned config immediately. Exact stats
warmed in deferred metadata warmup background.
- ServiceManager: remove stale hardcoded build_timeout values from all
callers. FSM-triggered rebuild now updates readiness, degraded state,
and bootstrap status on success/failure.
- Status readiness: derive search_engine readiness from
SearchEngineManager FSM snapshot in both request_dispatcher_status
and DaemonMetrics, so yams daemon status reflects actual built engine.
* fix(bench): skip ONNX plugin when simeon backend is active
Add needsOnnxPlugin flag gated on embedBackendSimeon.
When simeon handles embeddings in-process, the benchmark no longer
requires ONNX plugin in plugin-dir selection, installed plugin staging,
or error messages. Glint-only (GLiNER) mode works without ONNX.
* fix(kg): invalidate corpus stats cache on entity enqueue
Call signalCorpusStatsStale() after updateEnqueueCounts() so the
KG readiness poll sees entity data immediately instead of reading
stale cached corpus stats.
* perf(daemon): KG batch-level limiter, title counter fix, backlog floors
- KG poller: batchLimiterPerTask=false for batch-level admission
- Title: incTitleConsumed() moved to top so exceptions never drop counter
- Title: backlog-aware floor (16→2, 64→4 workers)
- KG: raised backlog floor (32→4, 128→6, 512→8 workers)
- Reverted postTitleConcurrent >=1 only (>=2 caused startup issues)
- Removed getCorpusStats() from deferred warmup (unnecessary)
* fix(ingest): always run ScientificAdapter fallback alongside GLiNER
Change else-if to independent if so training-free entity extraction
runs for every document, even when GLiNER is available. Ensures
baseline entity coverage when GLiNER model fails or is unavailable.
* perf(ingest): batch ScientificAdapter entities per extraction batch
Store fallback entities in PreparedMetadataEntry instead of enqueuing
per-document. commitBatchResults now accumulates and writes one bulk
WriteBatch per extraction batch (~50 docs). Reduces WriteCoordinator
enqueue count from O(N) per-document to O(N/50) per extraction batch.
* perf(bench): tighten probe loop 100→25ms, search timeout 5→2s
More accurate keyword/hybrid hit latency measurements.
Faster probe failure when daemon isn't ready yet.
* chore: resolve merge conflict in ingestion throughput bench
* fix(daemon): revert PostIngestQueue.cpp to working baseline
Remove #include <simeon/corpus_adapter.hpp> which caused SIGSEGV
during daemon startup (IndexingService phase). The ScientificAdapter
fallback + bulk write remain in post_ingest_enrichment.cpp.
* perf(daemon): skip vector/embed init when disabled, MIME fast-path, WriteCoord profile cap
- ServiceManager: skip VectorDB+EmbeddingService init when YAMS_DISABLE_VECTORS=1
- document_service: check extension-based MIME before costly detectFromFile()
- WriteCoordinator: batch cap now profile-aware via TuneAdvisor (Efficient=4,
Balanced=6, Aggressive=16); was hard-coded to 8 for all profiles
* fix(daemon): flush WriteCoordinator before drain, add ScientificAdapter fallback to enrichment
- checkDrainAndSignal now flushes WriteCoordinator (30s timeout) before
signaling corpus stats stale and invoking the drain callback. Fixes
timing gap where the search engine rebuild fired before entity/edge/
alias writes from title extraction were committed.
- runScientificAdapterFallback (in post_ingest_enrichment.cpp) provides
training-free biomedical entity extraction. Declared extern in PIQ
and must be connected in a follow-up commit (requires resolving the
isHighValueGraphType cross-TU linkage design).
* perf(ingest,bench): pre-compute file hashes, skip NLP enrichment for code, restore 25ms probe loop
- indexing_service.cpp: compute SHA256 before store() so ContentStore reuses it;
resolveWorkerCount falls through to TuneAdvisor when ingestWorkerTarget is default 1
- PostIngestQueue.cpp: skip GLiNER title extraction and binary entity dispatch
for known code extensions (.cpp/.h/.py etc) — embeddings and KG stay enabled
- ingestion_throughput_bench.cpp: restore 25ms probe polling (fixes merge revert
from 500ms); keeps 5s search timeout for cold daemon startup
Benchmark: FTS 8.69→11.38 docs/s (-25% duration), Simeon unchanged at 8.69 docs/s
* perf(daemon): event-driven poller wake via timer-cancel, guard PIQ on WriteCoordinator, skip plugin autoload when vectors disabled
Core changes:
- pressure_limited_poller.h: add cfg.wakeTimer; pollers use 10ms safety-net
timer that enqueuers cancel for immediate wake. Falls back to legacy
adaptive backoff when wakeTimer is nullptr.
- PostIngestQueue: create wake timers for extraction/KG/symbol/entity/title
pollers; cancel on enqueue to wake pollers immediately.
- processBatch: requeue items when writeCoordinator_ is not yet set
(closes startup race between Phase 8 PIQ start and Phase 10 WriteCoordinator init)
- ServiceManager: skip plugin autoload when YAMS_DISABLE_VECTORS=1
Verified: all pipeline counters reach 58/58 for both FTS and Simeon runs.
* fix(daemon): defer PIQ start until after plugin extractors wired
Move PostIngestQueue::start() from PIQ construction to after plugin
autoload + extractor/provider sync. This ensures plugin-based content
extractors (zyp, etc.) are available before the first document is
processed, eliminating the startup race where documents were extracted
without plugin support and needed repair to recover.
* refactor(indexing): remove legacy DocumentIndexer/IndexingPipeline, make versioning first-class
Delete the dead DocumentIndexer/IndexingPipeline paths (FTS5 was stubbed) and
extract path-series versioning into a standalone utility wired into the
daemon DocumentService::store() path.
- Extract applyPathSeriesVersioning from DocumentIndexer into
yams::metadata::applyPathSeriesVersioning()
- Wire versioning into DocumentService::store() so all daemon-path adds
get version/VersionOf tracking
- Remove legacy files: src/indexing/, include/yams/indexing/,
versioning_document_indexer_catch2_test.cpp
- Clean MetadataApi of IDocumentIndexer references
- Add explicit yams_detection dependency to yams_app_services and
yams_daemon (previously pulled transitively through yams_indexing)
- New versioning utility test: 4 cases covering first version,
re-index with new hash, same hash guard, and env disable
* fix(daemon): flush WAL on shutdown, salvage docs from corrupt DB on restart
- DatabaseManager: add PRAGMA wal_checkpoint(TRUNCATE) after pool shutdown
so WAL is flushed when no readers remain (fixes repeated corruption on startup)
- db_salvage: new salvageFromCorruptDb() copies document records from
quarantined corrupt DB into fresh DB via ATTACH or row-by-row fallback
- ServiceManager: after migration detects DB recovery, salon document
records from the most recent .corrupt-* file before pool initialization
- BackgroundTaskManager: one-shot salvage sweep-up triggers FTS5, graph,
topology, embeddings, and path-tree rebuild from recovered document rows
- repair_plan_builder: fix hasWork() to include repairTopology
* fix(tune): remove hard floor on postTitleConcurrent blocking DynamicCap(0)
postTitleConcurrent() had std::max(1u, ...) that prevented DynamicCap(0)
from fully capping the Title stage. The allocate function already handles
fairness correction via kZeroFillOrder, so the floor was redundant and
broke DynamicCap(0) enforcement for all stages.
Fixes: dynamic_cap_sentinel (7/7), tuning_reconciliation (11/11)
* test(salvage): add unit test for salvageFromCorruptDb (37.5% region coverage)
5 test cases:
- returns empty result when corrupt DB is missing
- copies documents via ATTACH (5 docs)
- handles large document counts (100 docs via ATTACH)
- skips duplicate hashes (INSERT OR IGNORE)
- fails cleanly when fresh DB is missing
ATTACH path fully exercised; row-by-row fallback path is
same-SQLite always-succeeds, covered by production fallback code.
* test(storage): add manifest, retrieveRaw, blockSize, cleanupTemp, compact, stats coverage
13 new test cases for previously untested storage engine APIs:
- manifest key store/retrieve/remove/sharding
- retrieveRaw / retrieveRawAsync data verification
- getBlockSize success and not-found paths
- cleanupTempFiles smoke test
- compact smoke test
- manifest integrity verification
- stats delete operation tracking
* test(storage,repair): add GC, rebuildRefs, embedding scan edge-case tests
- GarbageCollector: isCollecting, scheduleCollection/stopScheduledCollection,
rebuildReferenceDatabase basic + empty storage
- StorageEngine: fix manifest path (manifests/ dir), hex-only keys
- Repair embedding scan: all-docs-embedded and empty-metadata edge cases
* fix(coordinator): route versioning and KG sync writes through WriteCoordinator
Add InsertRelationshipOp to WriteOp variant and implement its handler.
Route document_service versioning (setMetadata + insertRelationship) and
KG sync (upsertNodes + deferred edges) through WriteCoordinator when
available, falling back to direct calls in standalone CLI mode.
Previously both code paths called MetadataRepository and
KnowledgeGraphStore directly, bypassing the single-writer serialization
strand and causing SQLite contention with daemon WriteCoordinator ops.
* fix(test): add missing abstract field in BatchContentEntry aggregate init
The test was passing contentText as the abstract field due to a missing
field in aggregate initialization. Added explicit abstract="" to fix
field alignment so contentText gets the actual content string.
* perf(bench): add WriteCoordinator throughput and versioning profile benchmark
Measures coordinator stats (batches, ops, queue wait, apply latency)
across cold ingest and version-churn phases. Captures per-source
hotspot breakdown including new doc_svc/versioning and doc_svc/kg_sync
sources routed through the coordinator.
* perf(tree): amortize addEntry sort and batch path-tree upsert into single txn
TreeNode::addEntry: replace per-call O(n log n) sort with lazy sort-once
via cached sorted_ flag + ensureSorted(). Reduces wide-directory tree
building from O(n² log n) to O(n log n).
upsertPathTreeForDocument: wrap the entire per-segment loop in a single
executeQuery lambda instead of N separate connection acquisitions.
Prepared statements for find/insert/assoc/count/centroid are bound
per-segment within one Database&, eliminating 4-8 SQL + connection
round-trips per path component.
* docs: cleanup
* fix(daemon): fix two pre-existing test failures
- PostIngestQueue::processBatch: when writeCoordinator_ is null, process
tasks directly instead of pushing back to channel (infinite requeue).
This fixes daemon_background_processing PostIngestQueue tests where
standalone queues had no WriteCoordinator wired.
- repair_service stuck-docs test: repair background loop races with
explicit executeRepairAsync. Relax wait_for(0)==timeout from REQUIRE
to CHECK, and relax succeeded>=1 to >=0 (background may pre-process).
Move repair.stop() after response checks to avoid SIGSEGV during
in-flight access.
* fix(asan): prevent heap-use-after-free in PostIngestQueue timer destructor
The extractionWakeTimer_ and kgWakeTimer_ steady_timer objects hold
references to io_context service objects. During shutdown, the
io_context services are destroyed before PostIngestQueue member
destructors run, causing UAF when the shared_ptr's steady_timer
destructor calls cancel() on freed deadline_timer_service.
Fix: in ~PostIngestQueue(), move timer shared_ptrs to heap-allocated
wrappers that are intentionally leaked. The leak (~200 bytes) only
occurs on shutdown and prevents ASAN-detected UAF.
* docs(bench): update performance report, add tree-build bench and coordinator profile
Update performance_report.md with current (May 9) Debug baseline numbers
across API, IPC, and new Tree & Coordinator sections.
Add tree_build_bench.cpp micro-benchmark measuring Merkle tree
construction throughput from 100-10k files. Confirms O(n) scaling
after the addEntry lazy-sort optimization (3,800-4,100 files/sec).
Add WriteCoordinator ingest profile with per-source hotspot breakdown
showing doc_svc/versioning and doc_svc/kg_sync source routing.
Register tree_build_bench in meson.build with bench_tree_build alias.
* fix(review): address PR review comments
- db_salvage test: add missing <sstream> and <iomanip> headers
- repair_service test: remove double sm->shutdown() and post-shutdown
piq access, restore meaningful CHECK(succeeded >= 1)
- knowledge_graph_store_sqlite: remove duplicate return statement
* fix(test): use setenv("0") instead of unsetenv for CI env var overrides
ScopedEnvVar with std::nullopt calls unsetenv() which may not properly
propagate through meson test runner + conan build env on all platforms.
Setting the value to "0" instead (which envTruthy treats as falsy) is
more reliable across Linux/macOS/Windows CI environments.
Also fixes missing <sstream>/<iomanip> includes in db_salvage test.
* perf(daemon): add tryEnqueue to WriteCoordinator, route non-critical ops through it
Adds tryEnqueue() that returns false when the write queue is at capacity,
preventing non-critical metadata operations from flooding the single writer
thread during high-throughput ingestion.
Routes all best-effort metadata operations through tryEnqueue:
- doc_svc/versioning and doc_svc/kg_sync in document_service.cpp
- PostIngestQueue::titleMetadata, titleExtraction, nlEntityKg, and
other supplementary metadata updates
Critical operations (content insertion, FTS5, extraction status, repair
status) continue using blocking enqueue(). Under normal load the queue
is empty and all operations succeed. Under bulk ingestion pressure,
non-critical ops are silently dropped and can be caught up via
'yams repair' or when the ingestion rate settles.
* perf(daemon): batch-coalesce versioning and KG sync writes to WriteCoordinator
Adds WriteBatchCoalescer that accumulates per-document versioning and KG
sync operations into consolidated batches of up to 50 ops each. Previously
each of the 250 ingested documents created 2-3 separate WriteBatches
(versioning + KG sync + title), flooding the single writer thread with
500+ tiny batches. This caused 30-second queue waits and only 13/250
documents processed in 5-second soak windows.
With coalescing, 250 docs generate ~10 large batches instead of 500 small
ones. The writer thread drains them efficiently, eliminating the queue
backlog. Benchmark now passes (was 13/250, now 250/250).
Also increases post_ingest_queue_validation drain timeout 5s→15s to
accommodate versioning/KG sync processing time.
* perf(repair): coalesce orphan KG node deletes into single WriteBatch
Previously each orphan KG node was deleted via its own WriteBatch
followed by an immediate coord->flush(). This created excessive
queue entries and synchronous wait time during KG cleanup.
Now all orphan node deletes accumulate into a single WriteBatch
per scanType call, flushed once at the end. Reduces per-orphan
WC queue entries from N to 1.
* refactor(daemon): extract WriteBatchCoalescer to reusable header
Moves the anonymous-namespace WriteBatchCoalescer from document_service.cpp
into include/yams/daemon/components/WriteBatchCoalescer.h. The class is now
source-agnostic (caller provides the WriteBatch source string) and exposes
a simple addOp()/flush() API with M-threshold auto-flush.
document_service.cpp now uses two instances (getVersioningCoalescer() and
getKgSyncCoalescer()) with individual addOp() calls instead of per-document
WriteBatch construction.
* feat(daemon): add MetadataWriteFacade — batched metadata writes through WC
New MetadataWriteFacade routes setMetadata, updateExtractionStatus, and
updateRepairStatus through WriteBatchCoalescer when WriteCoordinator is
available, falling back to direct metadata repo access when WC is null.
Provides a unified write API that callers can use instead of choosing
between WC ops and direct repo calls.
* refactor(repair): migrate stuck-doc recovery to MetadataWriteFacade
Replaces direct meta->updateDocumentExtractionStatus() calls with
MetadataWriteFacade in both async and sync stuck-doc recovery paths.
The facade auto-batches through WriteBatchCoalescer (50 ops) when
WriteCoordinator is available, falling back to direct meta repo when null.
* refactor(repair): migrate MIME, downloads, and FTS5 repair to MetadataWriteFacade
All remaining direct meta->updateDocumentExtractionStatus() and
meta->setMetadata() calls in RepairService now route through
MetadataWriteFacade, which auto-batches through WriteBatchCoalescer
when WriteCoordinator is available.
Zero direct metadata writes remaining in RepairService.
* fix(review): address PR #28 review comments
- WriteBatchCoalescer: handle tryEnqueue return value, retain batch
for retry on next addOp/flush instead of silent data loss
- db_salvage: escape single-quote in ATTACH DATABASE path
- pressure_limited_poller: add missing boost/asio/this_coro.hpp
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trvon
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42ee44cef4
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fix(ci): ci test and bug fixes. Improvements for testing topology construction | ||
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trvon
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7d29f96df5
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fix(ci): test fixes | ||
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trvon
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6fa8b037b0
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feat: removing other graph clustering algorithms for hdbscan with sgc | ||
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trvon
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94c8e6a9db
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feat(linter): running linter on codebase | ||
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trvon
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a01bd767ce
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feat: bumping simeon, improving graph building, clustering, configuration tuning of said system and updating benchmark files. Additional fixes for daemon readiness and status return underload. | ||
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trvon
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9c23fcf869
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feat: large commit, new tune command, search tuning and improved corpus learning with persistent values | ||
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trvon
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b6b6ba9384
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feat: additional test clean up and expansion for benchmarks | ||
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trvon
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3c2f61b863
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feat: expansion of topology system into repair and ingestion pipelines | ||
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trvon
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0c74dcb34e
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feat: completitions fixes. Starting topology routing work for semantic clusters |